Background
A useful workflow with dimensionality reduction (DR) is to be able to concatenate samples to view the consensus map for the completed DR analysis instead of visualizing each file separately.
In the Cytobank platform, we can combine events from different files in the Illustration Editor to virtually visualize the concatenated files in one plot.
Alternatively, if you wish to physically concatenate files, please refer to the R based concatenation tools in this support article.
Suggested Workflows
Virtual concatenation in the Illustration Editor
You may configure and run your dimensionality reduction (DR) analysis as usual with all the individual files from different groups and conditions in one experiment. Then navigate to the Illustration Editor within the completed DR experiment and create a dot or contour plot displaying the DR map. You can follow the guidelines to assess DR quality and run exploratory data analysis with DR listed in this support article.
To virtually concatenate some FCS files, navigate to the Plots menu and select the Concatenate option that better fits your illustration (Rows, Columns or All multi-file positions). Alternatively, navigate to the Layout menu, click on the arrow next to the Rows or Columns position and select Concatenated.
(Plots and Layout menus showing the access to the virtual concatenation tool.)
If you have set up the illustration’s layout using sample tags, you may want to concatenate the FCS files selecting Plots -> Concatenate -> All multi-file positions. This option will combine all possible FCS files that belong to the same categories described by dimensions selected in the layout. Alternatively, you can concatenate the Rows or the Columns. This option will combine all FCS files displayed in the rows or in the columns, respectively.
(Dimensionality reduction plots displaying three individual samples per condition on the left. DR plots showing All multi-files positions virtually concatenated on the right.)
When concatenation is completed, you can check which FCS files are concatenated in the plot by hovering the mouse over it.
(Mouse over the plot displays Plot settings menu and information regarding the FCS files displayed in the plot.)
Physically concatenated files using R based tools
If you desire to concatenate the FCS files, our recommendation is to run DR and then concatenate the resulting files after the DR run is complete. We do not recommend concatenating the files before the run, then including the concatenated and separated files simultaneously in the same DR analysis. This strategy is ill-advised because it will make the run time of the algorithm longer and may negatively affect results. Concatenating the results of a DR after the run has completed is the proper way to accomplish the same workflow.
To concatenate DR result files:
- Export data as FCS or spreadsheet files from whole files and/or gated populations
- Concatenate the files.
- Upload the concatenated files to a new experiment.
Please refer to the FCS Concatenation Tool for further instructions.
*For Research Use Only. Not for use in diagnostic procedures.